Buggy code:
public class MetaDataFile { public static void readFile ( Path file , HashMap < String , ArchiveEntry > entries , CombineArchive archive , boolean continueOnError , List < String > errors ) throws CombineArchiveException , IOException , ParseException , JDOMException { Document doc = null ; try { doc = Utils . readXmlDocument ( file ) ; } catch ( JDOMException e ) { LOGGER . error ( e , "cannot<seq2seq4repair_space>read<seq2seq4repair_space>manifest<seq2seq4repair_space>of<seq2seq4repair_space>archive" ) ; errors . add ( "cannot<seq2seq4repair_space>read<seq2seq4repair_space>manifest<seq2seq4repair_space>of<seq2seq4repair_space>archive.<seq2seq4repair_space>xml<seq2seq4repair_space>seems<seq2seq4repair_space>to<seq2seq4repair_space>be<seq2seq4repair_space>invalid." ) ; if ( ! continueOnError ) throw e ; return ; } catch ( IOException e ) { LOGGER . error ( e , "cannot<seq2seq4repair_space>read<seq2seq4repair_space>manifest<seq2seq4repair_space>of<seq2seq4repair_space>archive." ) ; errors . add ( "cannot<seq2seq4repair_space>read<seq2seq4repair_space>manifest<seq2seq4repair_space>of<seq2seq4repair_space>archive.<seq2seq4repair_space>io<seq2seq4repair_space>error." ) ; if ( ! continueOnError ) throw e ; return ; } List < Element > nl = Utils . getElementsByTagName ( doc . getRootElement ( ) , "Description" , rdfNS ) ; for ( int i = 0 ; i < ( nl . size ( ) ) ; i ++ ) { Element current = nl . get ( i ) ; String about = current . getAttributeValue ( "about" , rdfNS ) ; if ( about == null ) { LOGGER . error ( ( ( ( ( "meta<seq2seq4repair_space>description<seq2seq4repair_space>" + i ) + "<seq2seq4repair_space>in<seq2seq4repair_space>" ) + file ) + "<seq2seq4repair_space>does<seq2seq4repair_space>not<seq2seq4repair_space>contain<seq2seq4repair_space>an<seq2seq4repair_space>`about`<seq2seq4repair_space>value.<seq2seq4repair_space>so<seq2seq4repair_space>we<seq2seq4repair_space>cannot<seq2seq4repair_space>assign<seq2seq4repair_space>it<seq2seq4repair_space>to<seq2seq4repair_space>an<seq2seq4repair_space>entity." ) ) ; errors . add ( ( ( ( ( "meta<seq2seq4repair_space>description<seq2seq4repair_space>" + i ) + "<seq2seq4repair_space>in<seq2seq4repair_space>" ) + file ) + "<seq2seq4repair_space>does<seq2seq4repair_space>not<seq2seq4repair_space>contain<seq2seq4repair_space>an<seq2seq4repair_space>`about`<seq2seq4repair_space>value.<seq2seq4repair_space>so<seq2seq4repair_space>we<seq2seq4repair_space>cannot<seq2seq4repair_space>assign<seq2seq4repair_space>it<seq2seq4repair_space>to<seq2seq4repair_space>an<seq2seq4repair_space>entity." ) ) ; if ( ! continueOnError ) throw new CombineArchiveException ( ( ( ( ( "meta<seq2seq4repair_space>description<seq2seq4repair_space>" + i ) + "<seq2seq4repair_space>in<seq2seq4repair_space>" ) + file ) + "<seq2seq4repair_space>does<seq2seq4repair_space>not<seq2seq4repair_space>contain<seq2seq4repair_space>an<seq2seq4repair_space>`about`<seq2seq4repair_space>value.<seq2seq4repair_space>so<seq2seq4repair_space>we<seq2seq4repair_space>cannot<seq2seq4repair_space>assign<seq2seq4repair_space>it<seq2seq4repair_space>to<seq2seq4repair_space>an<seq2seq4repair_space>entity." ) ) ; continue ; } if ( ( about . equals ( "." ) ) || ( about . equals ( "//" ) ) ) { if ( ! ( MetaDataFile . addMetaToEntry ( archive , current , null ) ) ) LOGGER . warn ( "could<seq2seq4repair_space>not<seq2seq4repair_space>parse<seq2seq4repair_space>description<seq2seq4repair_space>for<seq2seq4repair_space>" , about ) ; continue ; } if ( about . startsWith ( ".//" ) ) about = about . substring ( 2 ) ; while ( about . startsWith ( "//" ) ) about = about . substring ( 1 ) ; about = "//" + about ; ArchiveEntry currentEntry = null ; String fragmentIdentifier = null ; <START_BUG> about = Paths . get ( about ) . normalize ( ) . toString ( ) ; <END_BUG> for ( ArchiveEntry entry : entries . values ( ) ) { if ( ( about . startsWith ( entry . getFilePath ( ) ) ) && ( ( ( about . length ( ) ) == ( entry . getFilePath ( ) . length ( ) ) ) || ( ( about . charAt ( entry . getFilePath ( ) . length ( ) ) ) == '#' ) ) ) { currentEntry = entry ; if ( ( ( about . length ( ) ) > ( entry . getFilePath ( ) . length ( ) ) ) && ( ( about . charAt ( entry . getFilePath ( ) . length ( ) ) ) == '#' ) ) fragmentIdentifier = about . substring ( ( ( entry . getFilePath ( ) . length ( ) ) - 1 ) ) ; break ; } } if ( currentEntry == null ) { LOGGER . error ( "found<seq2seq4repair_space>no<seq2seq4repair_space>entry<seq2seq4repair_space>for<seq2seq4repair_space>description<seq2seq4repair_space>" , i , "<seq2seq4repair_space>in<seq2seq4repair_space>" , file , "<seq2seq4repair_space>(about=" , about , ")." ) ; errors . add ( ( ( ( ( ( ( "found<seq2seq4repair_space>no<seq2seq4repair_space>entry<seq2seq4repair_space>for<seq2seq4repair_space>description<seq2seq4repair_space>" + i ) + "<seq2seq4repair_space>in<seq2seq4repair_space>" ) + file ) + "<seq2seq4repair_space>(about=" ) + about ) + ")." ) ) ; if ( ! continueOnError ) throw new CombineArchiveException ( ( ( ( ( ( ( "found<seq2seq4repair_space>no<seq2seq4repair_space>entry<seq2seq4repair_space>for<seq2seq4repair_space>description<seq2seq4repair_space>" + i ) + "<seq2seq4repair_space>in<seq2seq4repair_space>" ) + file ) + "<seq2seq4repair_space>(about=" ) + about ) + ")." ) ) ; continue ; } if ( ! ( MetaDataFile . addMetaToEntry ( currentEntry , current , fragmentIdentifier ) ) ) LOGGER . warn ( "could<seq2seq4repair_space>not<seq2seq4repair_space>parse<seq2seq4repair_space>description<seq2seq4repair_space>for<seq2seq4repair_space>" , about ) ; } } public static int addAllMetaToEntry ( Path file , ArchiveEntry entry ) throws IOException , JDOMException { } private static boolean addMetaToEntry ( MetaDataHolder entity , Element subtree , String fragmentIdentifier ) { } public static List < File > writeFiles ( File baseDir , HashMap < String , ArchiveEntry > entries , CombineArchive archive ) throws IOException , TransformerException { } public static List < File > writeFile ( File baseDir , HashMap < String , ArchiveEntry > entries , CombineArchive archive ) throws IOException , TransformerException { } private static File getMetaOutputFile ( File baseDir ) { } private static void exportMetaData ( MetaDataHolder entity , Element rdf ) { } }

Fix:
about = Utils . pathFixer ( Paths . get ( about ) . normalize ( ) . toString ( ) ) ;